I wish to adopt the Khan Academy Model of "Flip Teaching" (wikipedia) Teachers make study materials as easy to self-study as possible and students can study the lecture videos from home; When students truly come to class and spend time with the teacher, they spend more time discussing, going through difficult concepts, going through homework assignments, etc. Adapting this concept to biochemistry labs has a lot of challenges. But I wish this step by step biochemistry crash course schedule may help you accumulate sufficient background knowledge. When we meet at the lab, we can go through the real bench work rather than wander around basic biochemistry concepts!
The schedule is totally artificial, you don't have to follow it. The idea is to go through them quick and with high quality. High Quality is essential, because you probably only have this one chance to go through this large amount of material during your research with me or even your whole life time. To get an idea how each task may take, go to the google doc! I listed an estimated time requirement for each learning task. We will discuss routinely and go through the materials you have covered.
First Week:
2012. 05.12 Assignment Biology Animations as a starter!
Get to see how amazing biology is!
Check out the PCR song and the Ribosome Dancing as well@!
2012. 05.12 Assignment General Biology Knowledge, grasp these basic biology1A concepts.
It will form the fundamental language we will be communicating every day on!
2012.05.14 Assignment Macroview: Biofuel and Biorenewable Chemical Special Topics.
Get to learn the insights from top leaders in the whole biofuel and biorenewable chemical field! (including a lecture from our boss, Prof. Jay Keasling!)
Having the macroview gets you closer to reality.
Science is exciting, but we want direct impact from it as well!
2012.05.19 Assignment Polyketide Synthase Lecture Video (part1, part2, part3), the iBioseminar lecture video given by the Titan of our field!!!
Good for beginners, yet very insightful comments: I got new thoughts every time I watch this lecture!
Try to go through this video very carefully! It's the central of my research actually.
Do I need Chem3A and Chem3B in order to understand the chemistry? (view my correspondence)
Fatty Acid Synthase Background: I try to find a good lecture video on fatty acid biosynthesis. Unfortunately only come up with several, when combined are semi O.K. By going through them step by step, hopefully you may gain some understanding of the fatty acid biosynthesis. a. Fast Preview Video: b. "Boring" Details, with figures of the enzyme!part1part2part3part4c. Quick Recapturing of the chemical mechanisms involved:
Unfortunately it's copyrighted material. The 8 clips we got is all that is freely available. I checked our UC Berkeley video library and it was not in our library either. This quick assignment is meant to reintroduce part of the central dogma concept and to introduce you to the giants in the field. These are THE true leaders of biology, it's sometimes important just to hear them talk.
2. Biochemistry Basics.
This is a long knowledge list from Prof. Chris Anderson.
It goes step by step, transforming any one without any biochemistry background into some really good biochem students.
Once you read through this tutorial (which is achievable probably within 3-5 days). You possess the basic knowledge that allows you to appreciate some real bench work stuff as below.
Third Week
3. \Dropbox\Undergraduate Research Training\Crash Course
Check out the Lab Bootcamp 2011 folder!
Lab Bootcamp is a five day course designed to crush you through the basic wetlab techniques you will be using in the lab!
These are the bread and butter techniques of biotechnology and you will probably go through them hundreds of thousands of times during you research in JBEI.
I challenge you guys to follow the schedule and finish this course PPT sets. As for the lab protocols, directly reading through them can be boring.
BUT I suggest you guys go through them by watching some lab technique demonstration videos at the same time.
The protocols starts to make much more sense when you combine them with lab demonstration videos.
Watch these videos one by one, I picked these videos because of they are concise and are of high quality.
Fourth Week:
4. \Dropbox\Undergraduate Research Training\Crash Course iCLEM Lab Manual 3.0
There are questions in each section, you can start answer some questions and I can send you the answer keys if you want.
5. J5, advanced DNA assembly.
Much faster and much more powerful than the traditional restriction enzymes and DNA ligases. http://j5.jbei.org/j5manual/pages/1.html
Go through just the intro part, listed below:
Introduction to DNA assembly
The DNA assembly challenge
The traditional multiple cloning site approach
The BioBrick approach
The SLIC, Gibson and CPEC assembly methods (and GeneArt® Seamless Cloning), this part is most important! We will be using them a lot this summer.
The Golden Gate assembly method (and MoClo and GoldenBraid)
6. \Dropbox\Undergraduate Research Training\Crash Course Guide_to_Literature_Searches.pptx
Teachers make study materials as easy to self-study as possible and students can study the lecture videos from home; When students truly come to class and spend time with the teacher, they spend more time discussing, going through difficult concepts, going through homework assignments, etc.
Adapting this concept to biochemistry labs has a lot of challenges. But I wish this step by step biochemistry crash course schedule may help you accumulate sufficient background knowledge.
When we meet at the lab, we can go through the real bench work rather than wander around basic biochemistry concepts!
The schedule is totally artificial, you don't have to follow it. The idea is to go through them quick and with high quality.
High Quality is essential, because you probably only have this one chance to go through this large amount of material during your research with me or even your whole life time.
To get an idea how each task may take, go to the google doc! I listed an estimated time requirement for each learning task.
We will discuss routinely and go through the materials you have covered.
First Week:
2012. 05.12 Assignment
Biology Animations as a starter!
Get to see how amazing biology is!
Check out the PCR song and the Ribosome Dancing as well@!
2012. 05.12 Assignment
General Biology Knowledge, grasp these basic biology1A concepts.
It will form the fundamental language we will be communicating every day on!
2012.05.14 Assignment
Macroview: Biofuel and Biorenewable Chemical Special Topics.
Get to learn the insights from top leaders in the whole biofuel and biorenewable chemical field! (including a lecture from our boss, Prof. Jay Keasling!)
Having the macroview gets you closer to reality.
Science is exciting, but we want direct impact from it as well!
Second Week:
2012. 05.19 Assignment
More macroview: Obama administration's Bioeconomy Blueprint and EU commission report on bioeconomy.
If you are in biotech, you get to listen closely to what politicians say: Policy can greatly influence what you can do!
Also don't forget to subscribe to Biofuel Digest, a daily news letter to get updated news about our field!!
2012.05.19 Assignment
Polyketide Synthase Lecture Video (part1, part2, part3), the iBioseminar lecture video given by the Titan of our field!!!
Good for beginners, yet very insightful comments: I got new thoughts every time I watch this lecture!
Try to go through this video very carefully! It's the central of my research actually.
2012. 05.23 Assignment
1. Cracking the Code, a award winning science video that brief over the history of genetics.
You should listen to the awesome theme music!
You can play the whole list here. Each individual clip is also available below:
Peas In A Pod (1/3) - Cracking The Code episode 1
Microscopes And Mutants (1/5) - Cracking The Code episode 2
The DNA Obsession (1/5) - Cracking The Code episode 3
The Gene Machine (1/3) - Cracking The Code episode 4
Some New Tricks With DNA (1/3) - Cracking The Code episode 5
Reading The Book Of Life (1/3) - Cracking The Code episode 6
Understanding The Book Of Life (1/3) - Cracking The Code episode 7
The Seeds Of A New Era (1/5) - Cracking The Code episode 8
Unfortunately it's copyrighted material. The 8 clips we got is all that is freely available. I checked our UC Berkeley video library and it was not in our library either. This quick assignment is meant to reintroduce part of the central dogma concept and to introduce you to the giants in the field. These are THE true leaders of biology, it's sometimes important just to hear them talk.
2. Biochemistry Basics.
This is a long knowledge list from Prof. Chris Anderson.
It goes step by step, transforming any one without any biochemistry background into some really good biochem students.
Once you read through this tutorial (which is achievable probably within 3-5 days). You possess the basic knowledge that allows you to appreciate some real bench work stuff as below.
Third Week
3. \Dropbox\Undergraduate Research Training\Crash Course
Check out the Lab Bootcamp 2011 folder!
Lab Bootcamp is a five day course designed to crush you through the basic wetlab techniques you will be using in the lab!
These are the bread and butter techniques of biotechnology and you will probably go through them hundreds of thousands of times during you research in JBEI.
I challenge you guys to follow the schedule and finish this course PPT sets. As for the lab protocols, directly reading through them can be boring.
BUT I suggest you guys go through them by watching some lab technique demonstration videos at the same time.
The protocols starts to make much more sense when you combine them with lab demonstration videos.
Watch these videos one by one, I picked these videos because of they are concise and are of high quality.
Day1 related lab demo videos: Central Dogma (DNA->RNA->Protein), Pipetts, Lab equipments, DNA gel extraction, **PCR** Song (intro1, intro2, lab demo).
Day2 related lab demo videos: the cloning cycle, routine cloning, DNA transformation related, transformation by electroporation, Gel Purification,
Day3 related lab demo videos: Listen to Dr. Michael Smith (inventor of PCR mutagenesis talk about the invention), site directed mutagenesis, QuickChange, bench work
Day4 related lab demo videos: protein purification, Ni NTA as an example, DNA miniprep (background, bench work demo).
Day5 related lab demo videos: run a protein gel, Quick lecture by iBioSeminar Professor Nico Stuurman explain Fluorescence Microscopy.
Fourth Week:
4. \Dropbox\Undergraduate Research Training\Crash Course
iCLEM Lab Manual 3.0
There are questions in each section, you can start answer some questions and I can send you the answer keys if you want.
5. J5, advanced DNA assembly.
Much faster and much more powerful than the traditional restriction enzymes and DNA ligases.
http://j5.jbei.org/j5manual/pages/1.html
Go through just the intro part, listed below:
Introduction to DNA assembly
The DNA assembly challenge
The traditional multiple cloning site approach
The BioBrick approach
The SLIC, Gibson and CPEC assembly methods (and GeneArt® Seamless Cloning), this part is most important! We will be using them a lot this summer.
The Golden Gate assembly method (and MoClo and GoldenBraid)
6. \Dropbox\Undergraduate Research Training\Crash Course
Guide_to_Literature_Searches.pptx
7. Streptomyces
An energizing video about the colorful species - streptomyces
Intro facts about their genetics
Lab related